Spinal muscular atrophy (SMA) is the second most common fatal autosomal recessive disorder after cystic fibrosis, affecting approximately 1 in 6,000 to 10,000 live births. The disorder is characterized by hypotonia, proximal muscle weakness and respiratory distress due to degeneration of motor neurons in the spinal cord. SMA is caused by mutations in the survival motor neuron 1 (SMN1) gene, which is located on chromosome 5 at 5q11.2-13.3. The majority of affected individuals exhibit loss of the SMN1 gene, either by complete gene deletion or through a gene conversion event involving the adjacent SMN2 gene. The SMN2 gene differs from the SMN1 gene by a single nucleotide (840C>T) in exon 7 and lies in an inverted orientation in cis- with the SMN1 gene on chromosome 5. At least one copy of the SMN1 gene is indispensable for normal survival of motor neurons. In contrast, both copies of the SMN2 gene are dispensable as approximately 5-10% of normal individuals lack both copies of SMN2, though in some cases, the number of SMN2 copies can modulate the clinical phenotype.
The molecular diagnosis of SMA is generally accomplished through the detection of a homozygous deletion of SMN1. More than 95% of SMA patents have a homozygous deletion of SMN1 exon 7. Carrier testing for SMA, however, is particularly challenging for several reasons. Because the SMN1 gene is highly homologous to SMN2, abnormalities in the SMN1 gene can only be detected with carefully designed allele-specific assays. Further, in about 4% of the carrier population, a chromosomal alteration places both copies of the SMN1 gene on one chromosome and zero copies on the other (i.e., silent carrier or 2+0 genotype). Gene dosage analysis can determine the copy number of SMN1 to detect carrier status in individuals that are heterozygous for the absence of SMN1, but are ineffective for detecting silent carrier genotypes, where two copies of the SMN1 gene are present on only one chromosome. In addition, because the SMN1 and SMN2 genes are separated by a long distance (800 kb) on the same chromosome, linkage analysis of the chromosomal defect is difficult.